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- PDB-4het: Crystal structure of a putative glycoside hydrolase (BT3745) from... -

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Basic information

Entry
Database: PDB / ID: 4het
TitleCrystal structure of a putative glycoside hydrolase (BT3745) from Bacteroides thetaiotaomicron VPI-5482 at 2.10 A resolution
ComponentsHYPOTHETICAL GLYCOSIDE HYDROLASE
KeywordsHYDROLASE / Galactose-binding domain-like / xylanase / PF13201 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


BT2081, beta-jelly-roll domain / Immunoglobulin-like - #2340 / Putative carbohydrate metabolism domain / Putative carbohydrate metabolism domain superfamily / Putative carbohydrate metabolism domain / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PCMD domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical glycoside hydrolase (BT3745) from Bacteroides thetaiotaomicron VPI-5482 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL GLYCOSIDE HYDROLASE
B: HYPOTHETICAL GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9884
Polymers79,8632
Non-polymers1242
Water6,521362
1
A: HYPOTHETICAL GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9942
Polymers39,9321
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HYPOTHETICAL GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9942
Polymers39,9321
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.385, 180.385, 63.752
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HYPOTHETICAL GLYCOSIDE HYDROLASE


Mass: 39931.699 Da / Num. of mol.: 2 / Fragment: UNP residues 16-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3745, NP_812656.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A1C1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 16-374) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 16-374) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M magnesium nitrate, 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97923
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 9, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.1→29.522 Å / Num. all: 69380 / Num. obs: 69380 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.023 Å2 / Rsym value: 0.097 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.157.60.8382.43878651210.838100
2.15-2.217.60.6971.13739849310.697100
2.21-2.287.60.5771.33726749110.577100
2.28-2.357.60.4781.63538746580.478100
2.35-2.427.60.4141.93448445220.414100
2.42-2.517.60.3192.43385144400.319100
2.51-2.67.60.25433222042270.254100
2.6-2.717.60.2083.73143741180.208100
2.71-2.837.60.164.72989739150.16100
2.83-2.977.60.1285.92883937750.128100
2.97-3.137.60.17.32765436180.1100
3.13-3.327.60.0887.82576033770.088100
3.32-3.557.60.0837.72443332050.083100
3.55-3.837.60.0768.22253529550.076100
3.83-4.27.60.064102096527510.064100
4.2-4.77.60.059111909725050.059100
4.7-5.427.60.0738.71655921870.073100
5.42-6.647.50.0798.11407418780.079100
6.64-9.397.30.06410.21094514900.064100
9.39-29.5226.80.05512.254137960.05595.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.522 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 7.33 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.EXPERIMENTAL PHASES (MAD) WERE USED AS RESTRAINTS DURING STRUCTURE REFINEMENT. 6.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION WERE INCLUDED IN THE SOLVENT STRUCTURE. 7.RAMACHANDRAN OUTLIERS AT RESIDUES A106, A95 AND B95 ARE IN REGIONS THAT DO NOT HAVE WELL-DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 3508 5.1 %RANDOM
Rwork0.1782 ---
obs0.1797 69354 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 192.73 Å2 / Biso mean: 66.9896 Å2 / Biso min: 30.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20.66 Å20 Å2
2--1.32 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 8 362 5677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025516
X-RAY DIFFRACTIONr_bond_other_d0.0030.023684
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9617489
X-RAY DIFFRACTIONr_angle_other_deg0.99839056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8585714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05425.613253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41515935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8471516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026240
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021096
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 218 -
Rwork0.268 4708 -
all-4926 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6175-0.03460.34761.13290.64543.11950.051-0.1182-0.06520.15230.06410.0890.11790.1401-0.11510.0389-0.02480.02970.15240.04470.129361.9397-83.46557.8994
23.21220.17920.60182.73470.06682.1364-0.1640.27660.1425-0.43110.0848-0.0904-0.1488-0.01650.07920.0863-0.03520.03210.2179-0.00430.144395.9804-77.35646.3613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 374
2X-RAY DIFFRACTION2B30 - 374

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